Sonic's continuity was destined to fail the minute SEGA decided to split the series for Western/Eastern audiences. It's an utter mess. At this point in time, I generally concern myself less over the unexplained properties of the Chaos Emeralds in the classic games and am having loads more fun trying to figure out how the moon was repaired as if nothing had happened.
The moon is big enough that it will return to a spherical shape on its own. That, or it's because the into to StH was made by blur who hadn't worked on any of the previous games and thus didn't know it had happened.
You do realize how far those pieces flew, right? And even if they didn't, it would take a loooooooooooong time for that to happen, and if that was the case, it sure as sunshine wouldn't look the same.